[{"author":[{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"volume":8,"date_created":"2021-06-07T10:55:27Z","date_updated":"2021-12-14T08:29:57Z","pmid":1,"year":"2012","publisher":"Public Library of Science","department":[{"_id":"DaZi"}],"publication_status":"published","extern":"1","article_number":"e1002988","doi":"10.1371/journal.pgen.1002988","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002988","open_access":"1"}],"external_id":{"pmid":["23071449"]},"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"month":"10","oa_version":"Published Version","_id":"9497","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 8","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","status":"public","issue":"10","abstract":[{"text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes.","lang":"eng"}],"type":"journal_article","date_published":"2012-10-11T00:00:00Z","citation":{"short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988.","chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988","apa":"Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002988","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012.","ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988."},"publication":"PLoS Genetics","article_type":"original","article_processing_charge":"No","day":"11","scopus_import":"1"},{"doi":"10.1016/j.gde.2012.01.007","language":[{"iso":"eng"}],"external_id":{"pmid":["22336527"]},"quality_controlled":"1","month":"04","publication_identifier":{"issn":["0959-437X"]},"author":[{"first_name":"Jason T.","last_name":"Huff","full_name":"Huff, Jason T."},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"date_updated":"2021-12-14T08:32:38Z","date_created":"2021-06-08T08:58:52Z","volume":22,"year":"2012","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"DaZi"}],"extern":"1","date_published":"2012-04-01T00:00:00Z","publication":"Current Opinion in Genetics and Development","citation":{"chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.","mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138.","apa":"Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” Current Opinion in Genetics and Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007"},"article_type":"review","page":"132-138","article_processing_charge":"No","scopus_import":"1","oa_version":"None","_id":"9528","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","intvolume":" 22","abstract":[{"lang":"eng","text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory."}],"issue":"2","type":"journal_article"},{"volume":86,"date_updated":"2021-01-12T08:22:18Z","date_created":"2018-12-11T11:49:27Z","author":[{"first_name":"Samuel","last_name":"Bieri","full_name":"Bieri, Samuel"},{"full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Todadri","last_name":"Senthil","full_name":"Senthil, Todadri S"},{"first_name":"Patrick","last_name":"Lee","full_name":"Lee, Patrick"}],"publisher":"American Physical Society","intvolume":" 86","status":"public","publication_status":"published","title":"Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice","_id":"966","acknowledgement":"We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF).","year":"2012","extern":1,"publist_id":"6431","issue":"22","abstract":[{"lang":"eng","text":"Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario."}],"type":"journal_article","date_published":"2012-12-13T00:00:00Z","doi":"10.1103/PhysRevB.86.224409","quality_controlled":0,"citation":{"mla":"Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22, American Physical Society, 2012, doi:10.1103/PhysRevB.86.224409.","short":"S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012).","chicago":"Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevB.86.224409.","ama":"Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2012;86(22). doi:10.1103/PhysRevB.86.224409","ista":"Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22).","ieee":"S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22. American Physical Society, 2012.","apa":"Bieri, S., Serbyn, M., Senthil, T., & Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.86.224409"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1208.3231"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","day":"13","month":"12"},{"date_published":"2012-09-01T00:00:00Z","publication":"Molecular Ecology","citation":{"ista":"Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617.","apa":"Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x","ieee":"K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.","ama":"Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x","chicago":"Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x.","mla":"Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x.","short":"K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617."},"page":"4605 - 4617","day":"01","has_accepted_license":"1","scopus_import":1,"pubrep_id":"296","file":[{"relation":"main_file","file_id":"5304","date_created":"2018-12-12T10:17:47Z","date_updated":"2020-07-14T12:45:57Z","checksum":"c14ee4cb2a8ba9575bfd8a9bb7a883bb","file_name":"IST-2014-296-v1+1_4_wasps_revised3.pdf","access_level":"open_access","file_size":235820,"content_type":"application/pdf","creator":"system"},{"creator":"system","content_type":"application/pdf","file_size":41975,"file_name":"IST-2014-296-v1+2_4_wasps_Supporting2.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:48Z","date_updated":"2020-07-14T12:45:57Z","checksum":"f00afc5b887c8222014b57375b8caece","file_id":"5305","relation":"main_file"}],"oa_version":"Submitted Version","_id":"2968","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570","579"],"title":"A likelihood based comparison of population histories in a parasitoid guild","status":"public","intvolume":" 21","abstract":[{"lang":"eng","text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd."}],"issue":"18","type":"journal_article","doi":"10.1111/j.1365-294X.2012.05700.x","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"month":"09","author":[{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"last_name":"Melika","first_name":"George","full_name":"Melika, George"},{"first_name":"Graham","last_name":"Stone","full_name":"Stone, Graham"}],"related_material":{"record":[{"id":"13075","relation":"research_data","status":"public"}]},"date_updated":"2023-05-30T13:07:47Z","date_created":"2018-12-11T12:00:36Z","volume":21,"year":"2012","acknowledgement":"This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. ","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","file_date_updated":"2020-07-14T12:45:57Z","publist_id":"3746","ec_funded":1},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2968"}]},"author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Graham","last_name":"Stone","full_name":"Stone, Graham"},{"last_name":"Melika","first_name":"George","full_name":"Melika, George"}],"oa_version":"Published Version","date_updated":"2023-05-30T13:07:48Z","date_created":"2023-05-23T17:01:02Z","_id":"13075","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","ddc":["570"],"status":"public","abstract":[{"text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","date_published":"2012-06-08T00:00:00Z","doi":"10.5061/DRYAD.0G0FS","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}],"oa":1,"citation":{"ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS","ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.","apa":"Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. https://doi.org/10.5061/DRYAD.0G0FS","ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.","mla":"Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).","chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS."},"article_processing_charge":"No","day":"08","month":"06"},{"day":"26","article_processing_charge":"No","scopus_import":"1","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_published":"2012-11-26T00:00:00Z","publication":"Journal of the American Chemical Society","citation":{"short":"O. Chovnik, R. Balgley, J.R. Goldman, R. Klajn, Journal of the American Chemical Society 134 (2012) 19564–19567.","mla":"Chovnik, Olga, et al. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society, vol. 134, no. 48, American Chemical Society, 2012, pp. 19564–67, doi:10.1021/ja309633v.","chicago":"Chovnik, Olga, Renata Balgley, Joel R. Goldman, and Rafal Klajn. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja309633v.","ama":"Chovnik O, Balgley R, Goldman JR, Klajn R. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 2012;134(48):19564-19567. doi:10.1021/ja309633v","ieee":"O. Chovnik, R. Balgley, J. R. Goldman, and R. Klajn, “Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets,” Journal of the American Chemical Society, vol. 134, no. 48. American Chemical Society, pp. 19564–19567, 2012.","apa":"Chovnik, O., Balgley, R., Goldman, J. R., & Klajn, R. (2012). Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja309633v","ista":"Chovnik O, Balgley R, Goldman JR, Klajn R. 2012. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 134(48), 19564–19567."},"article_type":"original","page":"19564-19567","abstract":[{"lang":"eng","text":"We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light."}],"issue":"48","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13407","title":"Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets","status":"public","intvolume":" 134","month":"11","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"doi":"10.1021/ja309633v","language":[{"iso":"eng"}],"external_id":{"pmid":["23181449"]},"quality_controlled":"1","extern":"1","author":[{"full_name":"Chovnik, Olga","last_name":"Chovnik","first_name":"Olga"},{"full_name":"Balgley, Renata","last_name":"Balgley","first_name":"Renata"},{"full_name":"Goldman, Joel R.","first_name":"Joel R.","last_name":"Goldman"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"date_updated":"2023-08-08T07:51:10Z","date_created":"2023-08-01T09:47:42Z","volume":134,"year":"2012","pmid":1,"publication_status":"published","publisher":"American Chemical Society"},{"quality_controlled":"1","external_id":{"pmid":["22392681"]},"language":[{"iso":"eng"}],"doi":"10.1002/smll.201101882","publication_identifier":{"eissn":["1613-6829"],"issn":["1613-6810"]},"month":"03","publisher":"Wiley","publication_status":"published","pmid":1,"year":"2012","volume":8,"date_updated":"2023-08-08T07:55:10Z","date_created":"2023-08-01T09:47:55Z","author":[{"first_name":"Yonatan","last_name":"Ridelman","full_name":"Ridelman, Yonatan"},{"last_name":"Singh","first_name":"Gurvinder","full_name":"Singh, Gurvinder"},{"full_name":"Popovitz-Biro, Ronit","last_name":"Popovitz-Biro","first_name":"Ronit"},{"last_name":"Wolf","first_name":"Sharon G.","full_name":"Wolf, Sharon G."},{"last_name":"Das","first_name":"Sanjib","full_name":"Das, Sanjib"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"extern":"1","page":"654-660","article_type":"original","citation":{"chicago":"Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf, Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small. Wiley, 2012. https://doi.org/10.1002/smll.201101882.","mla":"Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small, vol. 8, no. 5, Wiley, 2012, pp. 654–60, doi:10.1002/smll.201101882.","short":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small 8 (2012) 654–660.","ista":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 8(5), 654–660.","ieee":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn, “Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,” Small, vol. 8, no. 5. Wiley, pp. 654–660, 2012.","apa":"Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., & Klajn, R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. Wiley. https://doi.org/10.1002/smll.201101882","ama":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 2012;8(5):654-660. doi:10.1002/smll.201101882"},"publication":"Small","date_published":"2012-03-12T00:00:00Z","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"scopus_import":"1","article_processing_charge":"No","day":"12","intvolume":" 8","title":"Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles","status":"public","_id":"13408","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","issue":"5","abstract":[{"text":"Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls.","lang":"eng"}]},{"article_processing_charge":"No","day":"15","scopus_import":"1","series_title":"LNCS","date_published":"2012-10-15T00:00:00Z","citation":{"short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182.","mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” Automated Technology for Verification and Analysis, vol. 7561, Springer, 2012, pp. 167–82, doi:10.1007/978-3-642-33386-6_14.","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In Automated Technology for Verification and Analysis, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-33386-6_14.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:10.1007/978-3-642-33386-6_14","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in Automated Technology for Verification and Analysis, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182.","apa":"Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In Automated Technology for Verification and Analysis (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-33386-6_14","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182."},"publication":"Automated Technology for Verification and Analysis","page":"167-182","abstract":[{"text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","_id":"10903","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 7561","title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data","status":"public","publication_identifier":{"eisbn":["9783642333866"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642333859"]},"month":"10","doi":"10.1007/978-3-642-33386-6_14","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","location":"Thiruvananthapuram, India","start_date":"2012-10-03","end_date":"2012-10-06"},"language":[{"iso":"eng"}],"quality_controlled":"1","place":"Berlin, Heidelberg","author":[{"full_name":"Bouajjani, Ahmed","last_name":"Bouajjani","first_name":"Ahmed"},{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi"},{"first_name":"Constantin","last_name":"Enea","full_name":"Enea, Constantin"},{"first_name":"Mihaela","last_name":"Sighireanu","full_name":"Sighireanu, Mihaela"}],"volume":7561,"date_created":"2022-03-21T07:58:39Z","date_updated":"2023-09-05T14:07:24Z","acknowledgement":"This work has been partially supported by the French ANR project Veridyc","year":"2012","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published"},{"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642330896"],"eisbn":["9783642330902"],"issn":["0302-9743"]},"month":"10","doi":"10.1007/978-3-642-33090-2_27","conference":{"name":"ESA: European Symposium on Algorithms","location":"Ljubljana, Slovenia","start_date":"2012-09-10","end_date":"2012-09-12"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08234"}],"oa":1,"external_id":{"arxiv":["1604.08234"]},"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"535"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"volume":7501,"date_created":"2022-03-21T08:01:45Z","date_updated":"2023-09-05T14:09:30Z","year":"2012","acknowledgement":"Supported by the Austrian Science Fund (FWF): P23499-N23, the Austrian Science Fund (FWF): S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2012-10-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” In Algorithms – ESA 2012, 7501:301–12. Springer, 2012. https://doi.org/10.1007/978-3-642-33090-2_27.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, Algorithms – ESA 2012, Springer, 2012, pp. 301–312.","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithms – ESA 2012, vol. 7501, Springer, 2012, pp. 301–12, doi:10.1007/978-3-642-33090-2_27.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” in Algorithms – ESA 2012, Ljubljana, Slovenia, 2012, vol. 7501, pp. 301–312.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2012). Polynomial-time algorithms for energy games with special weight structures. In Algorithms – ESA 2012 (Vol. 7501, pp. 301–312). Ljubljana, Slovenia: Springer. https://doi.org/10.1007/978-3-642-33090-2_27","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2012. Polynomial-time algorithms for energy games with special weight structures. Algorithms – ESA 2012. ESA: European Symposium on Algorithms, LNCS, vol. 7501, 301–312.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. In: Algorithms – ESA 2012. Vol 7501. Springer; 2012:301-312. doi:10.1007/978-3-642-33090-2_27"},"publication":"Algorithms – ESA 2012","page":"301-312","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time.\r\nIn this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10905","intvolume":" 7501","status":"public","title":"Polynomial-time algorithms for energy games with special weight structures"},{"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10906","title":"HSF(C): A software verifier based on Horn clauses","status":"public","intvolume":" 7214","abstract":[{"lang":"eng","text":"HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2012-04-01T00:00:00Z","publication":"Tools and Algorithms for the Construction and Analysis of Systems","citation":{"short":"S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.","mla":"Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:10.1007/978-3-642-28756-5_46.","chicago":"Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-28756-5_46.","ama":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. Tools and Algorithms for the Construction and Analysis of Systems. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:10.1007/978-3-642-28756-5_46","apa":"Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., & Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan & B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-28756-5_46","ieee":"S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in Tools and Algorithms for the Construction and Analysis of Systems, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551.","ista":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551."},"page":"549-551","day":"01","article_processing_charge":"No","scopus_import":"1","series_title":"LNCS","author":[{"full_name":"Grebenshchikov, Sergey","first_name":"Sergey","last_name":"Grebenshchikov"},{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","first_name":"Ashutosh"},{"full_name":"Lopes, Nuno P.","last_name":"Lopes","first_name":"Nuno P."},{"full_name":"Popeea, Corneliu","last_name":"Popeea","first_name":"Corneliu"},{"last_name":"Rybalchenko","first_name":"Andrey","full_name":"Rybalchenko, Andrey"}],"date_updated":"2023-09-05T14:09:54Z","date_created":"2022-03-21T08:03:30Z","volume":7214,"year":"2012","publication_status":"published","publisher":"Springer","editor":[{"full_name":"Flanagan, Cormac","last_name":"Flanagan","first_name":"Cormac"},{"last_name":"König","first_name":"Barbara","full_name":"König, Barbara"}],"department":[{"_id":"ToHe"}],"place":"Berlin, Heidelberg","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2012-04-01","start_date":"2012-03-24","location":"Tallinn, Estonia"},"doi":"10.1007/978-3-642-28756-5_46","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-642-28756-5_46"}],"oa":1,"quality_controlled":"1","month":"04","publication_identifier":{"isbn":["9783642287558"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783642287565"]}}]